MolNFT v1 · #135082 · protein

Structure of the tpr oligomerization domain

5TO6 · Nucleoprotein tpr: “Structure of the tpr oligomerization domain”. X-ray diffraction, 4 pockets (best druggability 0.63). MolNFT v1 #135082 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5TO6
Type: protein
Length: 560 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein tpr
UniProt: P12270
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 94% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoprotein tpr	protein	141	94% helix, 0% strand	P12270
B	Nucleoprotein tpr	protein	139	94% helix, 0% strand	P12270
C, D	Nucleoprotein tpr	protein	140	94% helix, 0% strand	P12270

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	560	0.63	0.75	49	empty
2	308	0.52	0.74	30	empty
3	265	0.48	0.73	23	empty
4	106	0.37	0.74	16	empty

Interfaces

6 interfaces between chains.

A–B · 3708 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 3622 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 656 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 622 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 136 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5TO6 · Structure of the TPR oligomerization domain · the same entry in another collection · chain A against A, TM-score 1.00
P12270 · AlphaFold monomer V2.0 prediction for nucleoprotein tpr (P12270) · a predicted model of the same protein · chain A against A, TM-score 0.72

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P12270
Elsewhere: RCSB PDB 5TO6 · PDBe 5TO6 · UniProt P12270

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